Variant 1-151133355-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_030913.6(SEMA6C):c.1922A>G(p.Glu641Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00706 in 1,599,422 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0072 ( 59 hom. )

Consequence

SEMA6C
NM_030913.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.71

Variant links:

Genes affected

SEMA6C (HGNC:10740): (semaphorin 6C) This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]

SEMA6C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0051748753).

BP6

Variant 1-151133355-T-C is Benign according to our data. Variant chr1-151133355-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3067221.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA6C	NM_030913.6 linkuse as main transcript	c.1922A>G	p.Glu641Gly	missense_variant	19/19	ENST00000368914.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA6C	ENST00000368914.8 linkuse as main transcript	c.1922A>G	p.Glu641Gly	missense_variant	19/19	1	NM_030913.6	P4	Q9H3T2-1
SEMA6C	ENST00000368913.7 linkuse as main transcript	c.2018A>G	p.Glu673Gly	missense_variant	20/20	1		A1	Q9H3T2-3
SEMA6C	ENST00000341697.7 linkuse as main transcript	c.1922A>G	p.Glu641Gly	missense_variant	19/19	1		P4	Q9H3T2-1
SEMA6C	ENST00000368912.7 linkuse as main transcript	c.1898A>G	p.Glu633Gly	missense_variant	19/19	1			Q9H3T2-2

Frequencies

GnomAD3 genomes

AF:

0.00552

AC:

838

AN:

151942

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00138

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.0107

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00892

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00442

AC:

967

AN:

218692

Hom.:

AF XY:

0.00449

AC XY:

540

AN XY:

120378

show subpopulations

Gnomad AFR exome

AF:

0.00121

Gnomad AMR exome

AF:

0.00171

Gnomad ASJ exome

AF:

0.000107

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000896

Gnomad FIN exome

AF:

0.00726

Gnomad NFE exome

AF:

0.00764

Gnomad OTH exome

AF:

0.00474

GnomAD4 exome

AF:

0.00722

AC:

10453

AN:

1447360

Hom.:

Cov.:

AF XY:

0.00699

AC XY:

5027

AN XY:

719606

show subpopulations

Gnomad4 AFR exome

AF:

0.00117

Gnomad4 AMR exome

AF:

0.00200

Gnomad4 ASJ exome

AF:

0.000193

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00106

Gnomad4 FIN exome

AF:

0.00797

Gnomad4 NFE exome

AF:

0.00857

Gnomad4 OTH exome

AF:

0.00602

GnomAD4 genome

AF:

0.00550

AC:

837

AN:

152062

Hom.:

Cov.:

AF XY:

0.00553

AC XY:

411

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.00137

Gnomad4 AMR

AF:

0.00268

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.0107

Gnomad4 NFE

AF:

0.00891

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00684

Hom.:

Bravo

AF:

0.00461

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.000685

AC:

ESP6500EA

AF:

0.00549

AC:

ExAC

AF:

0.00475

AC:

569

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

SEMA6C: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Uncertain

0.040

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.39

.;.;T;T

Eigen

Uncertain

0.23

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.89

LIST_S2

Uncertain

0.86

D;D;.;D

MetaRNN

Benign

0.0052

T;T;T;T

MetaSVM

Benign

-0.77

MutationAssessor

Uncertain

2.5

.;.;M;M

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Pathogenic

0.82

PROVEAN

Uncertain

-3.9

D;D;D;D

REVEL

Uncertain

0.29

Sift

Benign

0.038

D;D;D;D

Sift4G

Uncertain

0.0020

D;D;D;D

Polyphen

0.038

B;D;D;D

Vest4

0.26

MVP

0.75

MPC

1.0

ClinPred

0.020

GERP RS

3.9

Varity_R

0.46

gMVP

0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over